Variant report

Variant	rs12481707
Chromosome Location	chr20:1453457-1453458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1449411..1451368-chr20:1451842..1453963,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NSFL1C-1	chr20:1453434-1453657	NONHSAT078117

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12480584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	1.00[JPT][hapmap]
rs17793360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	1.00[JPT][hapmap]
rs1884393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064645	1.00[JPT][hapmap]
rs2064646	1.00[JPT][hapmap]
rs2273321	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2873522	1.00[JPT][hapmap]
rs3829697	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275406	1.00[ASN][1000 genomes]
rs6033935	1.00[JPT][hapmap]
rs6105101	1.00[JPT][hapmap]
rs6109984	1.00[JPT][hapmap]
rs6109989	1.00[JPT][hapmap]
rs8118710	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123855	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984498	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12481707	FKBP1A	cis	multi-tissue	Pritchard
rs12481707	PSMF1	cis	parietal	SCAN
rs12481707	KLF5	trans	lymphoblastoid	seeQTL
rs12481707	ASRGL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1448200-1455800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:1448200-1457400	Weak transcription	Spleen	Spleen
3	chr20:1448200-1459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:1449000-1453600	Enhancers	Primary B cells from cord blood	blood
5	chr20:1449000-1454800	Enhancers	Fetal Intestine Small	intestine
6	chr20:1449400-1454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:1449400-1454200	Enhancers	K562	blood
8	chr20:1449800-1453800	Genic enhancers	Monocytes-CD14+_RO01746	blood
9	chr20:1450400-1453800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr20:1450400-1459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:1450400-1459000	Weak transcription	Lung	lung
12	chr20:1450600-1454600	Weak transcription	Right Ventricle	heart
13	chr20:1450800-1454000	Weak transcription	Adipose Nuclei	Adipose
14	chr20:1450800-1456200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr20:1450800-1458200	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr20:1451000-1454000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr20:1451200-1453800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr20:1451200-1454800	Enhancers	Fetal Intestine Large	intestine
19	chr20:1451200-1456000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr20:1451400-1453600	Weak transcription	GM12878-XiMat	blood
21	chr20:1451600-1453800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:1451600-1454000	Weak transcription	Small Intestine	intestine
23	chr20:1451600-1455600	Weak transcription	Placenta	Placenta
24	chr20:1451600-1459000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:1451800-1455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:1452000-1454000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:1452000-1454000	Weak transcription	A549	lung
28	chr20:1452000-1454000	Weak transcription	Osteobl	bone
29	chr20:1452000-1455200	Weak transcription	NHEK	skin
30	chr20:1452000-1455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:1452000-1459000	Weak transcription	HUVEC	blood vessel
32	chr20:1452000-1459000	Weak transcription	NH-A	brain
33	chr20:1452200-1454200	Enhancers	Primary B cells from peripheral blood	blood
34	chr20:1452200-1454200	Enhancers	Esophagus	oesophagus
35	chr20:1452400-1454600	Enhancers	Duodenum Mucosa	Duodenum
36	chr20:1452400-1454600	Weak transcription	HMEC	breast
37	chr20:1452600-1454400	Enhancers	Primary hematopoietic stem cells	blood
38	chr20:1452800-1453800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr20:1452800-1454400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr20:1452800-1454400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:1453000-1454200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr20:1453000-1454400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
43	chr20:1453000-1454400	Enhancers	Stomach Mucosa	stomach
44	chr20:1453200-1453600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr20:1453200-1453600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr20:1453200-1453800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr20:1453200-1454600	Bivalent Enhancer	HepG2	liver

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